Added

• #718 - Add support for independent long-read metagenomic assembly (requested by @ljmesi and many others, added by @muabnezor)
• #718 - Added metaMDBG and (meta)Flye as long read assemblers (added by @muabnezor)
• #718 - Added host removal for long reads using minimap2 as aligner (added by @muabnezor)
• #827 - Added nf-test CI testing for all test profiles (added by @jfy133)
• #829 - Add --skip_shortread_qc and --skip_longread_qc params for skipping certain default preprocessing steps (added by @erikrikarddaniel)
• #846 - Improve documentation of group samplesheet column (added by @vinisalazar)
• #855 - Add basic nf-tests for test_longreadonly, test_longreadonly_alternatives, test_hybrid and test_assembly_input (added by @dialvarezs)
• #864 - Add --gtdbtk_skip_aniscreen to disable fast classification of genomes by ANI using skani in GTDB-Tk (by @jfy133 and @prototaxites).

Changed

• #718 - Refactored all assembly steps into subworkflows (added by @muabnezor)
• #799 - Add --cat_classify_unbinned, to enable taxonomic classification of unbinned contigs using CAT (requested by @amizeranschi, added by @dialvarezs)
• #799 - Upgraded to latest version of CAT_pack modules (requested by @maxibor, added by @dialvarezs)
• #811 - Update util modules, and remove aria2 module to replace with native Nextflow downloading of CheckM database (by @dialvarezs)
• #816 - Removed all leftover references to conda 'defaults' channel (by @jfy133)
• #823 - Updated to nf-core 3.3.1TEMPLATE (by @jfy133 )
• #827 - Updated to nf-core 3.3.2TEMPLATE (by @dialvarezs)
• #841 - MultiQC config updated to support CheckM, CheckM2, and GTDB-Tk (by @harper357)
• #844 - Change loading mechanism of internal PhiX/Lambda databases to improve Dev UX when schema building (by @jfy133)
• #851 - Improve structure of local modules and subworkflows (by @dialvarezs)
• #853 - Update nf-core modules and subworkflows (by @dialvarezs)
• #856 - Update more nf-core modules (by @dialvarezs)

Fixed

• #843 - Fixed issue with large format Bowtie2 index files not being emitted from index module (reported by Nick Eckersley, fix by @jfy133)
• #847 - Allow the BBNorm process to use only 0.8 of the memory allocated to the task to stop if from oversubscribing memory (reported by and fix by @erikrikarddaniel)
• #850 - Fixed some modules of the GDTBTk subworkflow not being represented in version lists (fix by @jfy133)
• #852 - Fixed version reporting by ensure all modules are represented in final version.yml for MultiQC (by @jfy133)
• #854 - Update porechop/abi to a patched version to prevent duplicated read names (reported by @palec87, fix by @jfy133)
• #858 - Fix a single parameter validation failure reporting errors for all parameters by updated nf-schema to 2.5.1 (reported by @Pranjal-Bioinfo, fix by @nvnieuwk and @jfy133)
• #864 - Fix missing multi-threading of MetaEuk easypredict (reported by @OlivierCoen, fix by @prototaxites).

Dependencies

Deprecated

• #799 - Removed --cat_official_taxonomy in favour of --cat_allow_unofficial_lineages to control CAT's use of unofficial lineages (added by @dialvarezs)
• #825 - Removed --centrifuge_db, --kraken2_db, --krona_db and --skip_krona parameters following the removal of taxonomic profiling functionality. See nf-core/taxprofiler for replacement (added by @dialvarezs)
• #851 - Remove POOL_READ_* local modules in favor of nf-core cat/fastq (by @dialvarezs)
• #855 - Remove test_adapterremoval, test_ancient_dna, test_bbnorm, test_busco_auto, test_host_rm, test_hybrid_host_rm, test_binrefinement, test_concoct and test_longread profiles (added by @dialvarezs)
• #864 - Remove --gtdb_mash due to dropping of support by GTDBTk itself (by @prototaxites and @jfy133)